I currently only have 1 duplex, however I want to set this up right so it will work for any size portfolio.Currently I haveHome folder>multi family/single family/legal documentsInside the multi family I have Name of property-> general property maintenance/first floor/second floor Inside of first floor (the one currently rented)I have, pictures (before and will have after) / lease documents / a spreadsheet with each month, what day rent was paid, if it was late, if late was fee paid?

Humans can be paid a finders fee in California. 

Even if they pay late sometimes, you have a late fee to compensate you.

I guess the purpose for this is to help fund community improvements and maintenance though it's a bit unusual since HOA fees and property taxes typically cover these.

Check fees, as agencies usually charge a percentage of what they recover.Thank you! 

Because we don't refund application fees. 

What's a reasonable fee?

More likely, he is hoping to use the extra time to collect more rents and thus more fees to generate the funds to pay his owner clients:(

Right now I am paying about $6000 to $8000 to have 20 soil borings taken to a depth of 20 feet.The permit fees you are asking about are relatively cheap.

We have lots of automated processes - All online rent collections, inquiries, signature requests, and late fees.